I only know of one boat persay and that would be the selbina mhuara boat. There is various ferrys in area like carpenters landing that move you small distances. Some info reguarding where you need to go would be helpful. If you are trying to get to the dunes for subjob and lvl 10-20 you must go there via boat in mhuara. From wind woods go east sarta north to canyon then east to bubu penn. once in penn cross map going east then south to mhuara. Boat ride is 100 gil and if you are of and level lower than 37 I strongly recommend hiding in the cargo room on the lower floor of ship. There is a sea horror that kills most swiftly, not to mention random pirate attacks. You could also make a party and get your sub job in bubu penn but very few people do it.

try heavens tower or the building across from ah in lower jeuno.

to change alligence you must go into windhurst walls, and then into heavens tower, in there you should find a room with 3 tarus behind a desk, one of them asks you if you want to switch your alligence, but this will not work if you are currently involved in a mission

you get it when you reach rank 5, the nice Grand Duke of Jeuno gives it to you :)